Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.
Highlights
Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants
Research attempting to identify correlations between genetic diversity and phenotypic differences has primarily focused on the major strain types [12,13,14,15]
Genomic characterization of five newly isolated M. avium subsp. paratuberculosis strains in Korea Genome sequencing was conducted with five M. avium subsp. paratuberculosis (MAP) strains that were isolated from Korea as previously described [18]
Summary
Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies [4, 5]. MAP strains are differentiated into two major groups, known as “Cattle type” or “C-type” and “Sheep type” or “S-type”, which are named after the host species of first isolation [6]. Some molecular typing techniques have been developed, such as variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) and multilocus short sequence repeat (MLSSR), to elucidate the genetic diversity and investigate the molecular epidemiology of MAP strains [8, 9]. Research attempting to identify correlations between genetic diversity and phenotypic differences has primarily focused on the major strain types [12,13,14,15]
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